King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887

Cheng K, Burdine R, Dickinson M, Ekker S, Lin A, Lloyd K, Lutz C, MacRae C, Morrison J, O’Connor D, Postlethwait J, Rogers C, Sanchez S, Simpson J, Talbot W, Wallace D, Weimer J, Bellen H. Promoting validation and cross-phylogenetic integration in model organism research. Dis Model Mech. 2022;15(9). PMCID: PMC9531892

Lizewski R, Sealfon R, Park S, Smith G, Porter C, Gonzalez-Reiche A, Ge Y, Miller C, Goforth C, Pincas H, Termini M, Ramos I, Nair V, Lizewski S, Alshammary H, Cer R, Chen H, George M-C, Arnold C, Glang L, Long K, Malagon F, Marayag J, Nunez E, Rice G, Ana E, Schilling M, Smith D, Sugiharto V, Sun P, van de Guchte A, Khan Z, Dutta J, Vangeti S, Voegtly L, Weir D, Metcalf J, Troyanskaya O, Bishop-Lilly K, Grenfell B, van Bakel H, Letizia A, Sealfon S. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology. 2022;33(6):797–807. PMCID: PMC9531985

Yang D, Jones M, Naranjo S, Rideout W, Min K, Ho R, Wu W, Replogle J, Page J, Quinn J, Horns F, Qiu X, Chen M, Freed-Pastor W, McGinnis C, Patterson D, Gartner Z, Chow E, Bivona T, Chan M, Yosef N, Jacks T, Weissman J. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell. 2022;185(11):1905–1923.e25. PMCID: PMC9452598

Eickhoff M, Fei C, Cong J-P, Bassler B. LuxT Is a Global Regulator of Low-Cell-Density Behaviors, Including Type III Secretion, Siderophore Production, and Aerolysin Production, in Vibrio harveyi. mBio. 2022;13(1):e0362121. PMCID: PMC8764538

King S, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021;17(11):e1009560. PMCID: PMC8601562

Behnke M, Khan A, Lauron E, Jimah J, Wang Q, Tolia N, Sibley D. Rhoptry Proteins ROP5 and ROP18 Are Major Murine Virulence Factors in Genetically Divergent South American Strains of Toxoplasma gondii. PLoS Genet. 2015;11(8):e1005434. PMCID: PMC4546408

Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics. 2021;37(Suppl_1):i133-i141. PMCID: PMC8275333

Eickhoff M, Fei C, Huang X, Bassler B. LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA. PLoS Genet. 2021;17(4):e1009336. PMCID: PMC8043402

Letizia A, Ramos I, Obla A, Goforth C, Weir D, Ge Y, Bamman M, Dutta J, Ellis E, Estrella L, George M-C, Gonzalez-Reiche A, Graham W, van de Guchte A, Gutierrez R, Jones F, Kalomoiri A, Lizewski R, Lizewski S, Marayag J, Marjanovic N, Millar E, Nair V, Nudelman G, Nunez E, Pike B, Porter C, Regeimbal J, Rirak S, Ana E, Sealfon R, Sebra R, Simons M, Soares-Schanoski A, Sugiharto V, Termini M, Vangeti S, Williams C, Troyanskaya O, van Bakel H, Sealfon S. SARS-CoV-2 Transmission among Marine Recruits during Quarantine. N Engl J Med. 2020;383(25):2407–2416. PMCID: PMC7675690

Doane M, Morris M, Papudeshi B, Allen L, Pande D, Haggerty J, Johri S, Turnlund A, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery A, Lima L, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards R, Dinsdale E. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome. 2020;8(1):93. PMCID: PMC7293782

Moore G, Gitai Z. Both clinical and environmental Caulobacter species are virulent in the Galleria mellonella infection model. PLoS One. 2020;15(3):e0230006. PMCID: PMC7067423

Aardema M, vonHoldt B, Fritz M, Davis S. Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes. Parasit Vectors. 2020;13(1):8. PMCID: PMC6950815

Tianero M, Balaich J, Donia M. Localized production of defence chemicals by intracellular symbionts of Haliclona sponges. Nat Microbiol. 2019;4(7):1149–1159. PMCID: PMC8647704

Wang R, Seyedsayamdost M. Roseochelin B, an Algaecidal Natural Product Synthesized by the Roseobacter Phaeobacter inhibens in Response to Algal Sinapic Acid. Org Lett. 2017;19(19):5138–5141. PMID: 28920692

Charruau P, Johnston R, Stahler D, Lea A, Snyder-Mackler N, Smith D, vonHoldt B, Cole S, Tung J, Wayne R. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol. 2016;33(8):1967–78. PMCID: PMC5854094

De-Silva D, Mota L, Chazot N, Mallarino R, Silva-Brandão K, Piñerez L, Freitas A, Lamas G, Joron M, Mallet J, Giraldo C, Uribe S, Särkinen T, Knapp S, Jiggins C, Willmott K, Elias M. North Andean origin and diversification of the largest ithomiine butterfly genus. Sci Rep. 2017;7:45966. PMCID: PMC5384087

Whinnett A, Zimmermann M, Willmott K, Herrera N, Mallarino R, Simpson F, Joron M, Lamas G, Mallet J. Strikingly variable divergence times inferred across an Amazonian butterfly ’suture zone’. Proc Biol Sci. 2005;272(1580):2525–33. PMCID: PMC1599783

Mallarino R, Bermingham E, Willmott K, Whinnett A, Jiggins C. Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes. Mol Phylogenet Evol. 2005;34(3):625–44. PMID: 15683934

Jiggins C, Mallarino R, Willmott K, Bermingham E. The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera: nymphalidae). Evolution. 2006;60(7):1454–66. PMID: 16929662

Mallarino R, Campàs O, Fritz J, Burns K, Weeks O, Brenner M, Abzhanov A. Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. Proc Natl Acad Sci U S A. 2012;109(40):16222–7. PMCID: PMC3479598

Mallarino R, Abzhanov A. Paths less traveled: evo-devo approaches to investigating animal morphological evolution. Annu Rev Cell Dev Biol. 2012;28:743–63. PMCID: PMC8845070

McCulloch K, Yuan F, Zhen Y, Aardema M, Smith G, Llorente-Bousquets J, Andolfatto P, Briscoe A. Sexual Dimorphism and Retinal Mosaic Diversification following the Evolution of a Violet Receptor in Butterflies. Mol Biol Evol. 2017;34(9):2271–2284. PMID: 28505307

Guo C-J, Chang F-Y, Wyche T, Backus K, Acker T, Funabashi M, Taketani M, Donia M, Nayfach S, Pollard K, Craik C, Cravatt B, Clardy J, Voigt C, Fischbach M. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017;168(3):517–526.e18. PMCID: PMC5302092

Inclan Y, Persat A, Greninger A, Von Dollen J, Johnson J, Krogan N, Gitai Z, Engel J. A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa. Mol Microbiol. 2016;101(4):590–605. PMCID: PMC4980298

Aardema M, Andolfatto P. Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies. Evolution. 2016;70(8):1913–21. PMCID: PMC4980202

vonHoldt B, Takuno S, Gaut B. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012;29(10):3193–203. PMID: 22593226

Nadimpalli S, Persikov A, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015;11(3):e1005011. PMCID: PMC4351887

Jenni S, Goyal Y, von Grotthuss M, Shvartsman S, Klein D. Structural Basis of Neurohormone Perception by the Receptor Tyrosine Kinase Torso. Mol Cell. 2015;60(6):941–52. PMID: 26698662

Brown J, McBride C, Johnson P, Ritchie S, Paupy C, Bossin H, Lutomiah J, Fernandez-Salas I, Ponlawat A, Cornel A, Black W, Gorrochotegui-Escalante N, Urdaneta-Marquez L, Sylla M, Slotman M, Murray K, Walker C, Powell J. Worldwide patterns of genetic differentiation imply multiple ’domestications’ of Aedes aegypti, a major vector of human diseases. Proc Biol Sci. 2011;278(1717):2446–54. PMCID: PMC3125627

Matthews B, McBride C, DeGennaro M, Despo O, Vosshall L. The neurotranscriptome of the Aedes aegypti mosquito. BMC Genomics. 2016;17:32. PMCID: PMC4704297

Schumer M, Cui R, Powell D, Rosenthal G, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol. 2016;25(11):2661–79. PMID: 26937625

Kwan J, Tianero M, Donia M, Wyche T, Bugni T, Schmidt E. Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella. PLoS One. 2014;9(5):e95850. PMCID: PMC4008419

Williams B, Van Benschoten A, Cimermancic P, Donia M, Zimmermann M, Taketani M, Ishihara A, Kashyap P, Fraser J, Fischbach M. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014;16(4):495–503. PMCID: PMC4260654